Gaffer Tape said:but I think most people familiar with it can agree that it's considered harmless humor nowadays.
I think C3PX already meant to communicate that and I'd be perfectly willing to believe that most people who use it mean nothing (as with a lot of popular phrases with bad origins). However, the phrase itself sounds like it might have been primarily negative in some way (at some time). I found another version (which people on the interwebs say is even more popular) that goes "I'll beat you like a red headed stepchild." That one definitely seems to have at least a tiny degree of hostility. :)
Either way, this is interesting. If I can find something more substantial that would be cool.